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Evolutionary stability of a refactored phage genome.

Rachael Springman1, Ian J Molineux, Chanan Duong

  • 1Section of Integrative Biology, The University of Texas at Austin, Austin, TX 78712, USA.

ACS Synthetic Biology
|March 23, 2013
PubMed
Summary

Synthetic biology aims to create stable engineered genetic systems. This study shows that experimental evolution can help identify and overcome design problems in refactored bacteriophage T7, improving system stability.

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Area of Science:

  • Synthetic biology
  • Molecular biology
  • Genetics

Background:

  • Engineered genetic systems often exhibit instability due to fitness costs associated with introduced elements.
  • Synthetic biology seeks to predict and prevent detrimental engineering outcomes, but context-dependent element effects are not well understood.
  • Previous refactoring of bacteriophage T7 genome (30%) introduced 65 sequences, potentially impacting translational efficiency and regulatory functions.

Purpose of the Study:

  • To investigate the fitness effects and evolutionary dynamics of a refactored bacteriophage T7 genome under adaptive evolution.
  • To identify specific synthetic design challenges and evaluate the potential of experimental evolution for overcoming them.

Main Methods:

  • Adaptation of refactored bacteriophage T7 for rapid growth in two distinct environments.
  • Monitoring of phage fitness and sequence evolution during experimental adaptation.
  • Analysis of retained, lost, or modified synthetic design elements in evolved phages.

Main Results:

  • Refactoring initially imposed significant fitness costs, but these were largely recovered upon adaptation.
  • Evolved phages retained 60-70% of the synthetic design elements, indicating minor fitness impacts for most.
  • Element loss occurred, with some elements lost in parallel across different adaptation conditions, though direct correlates were not identified.

Conclusions:

  • Experimental evolution is a valuable approach for identifying specific synthetic design problems in engineered genetic systems.
  • The findings suggest that combining experimental evolution with alternative engineering strategies may be effective in enhancing the stability of synthetic biological constructs.
  • Most refactoring elements had minor fitness effects, and adaptation strategies can mitigate initial fitness costs.